Hello ,
I am currently working on 30 Affymetrix arrays for a time course
experiment using Limma package. I have two groups (A and B) with
samples taken at 0hr, 1hr, 6hr, 12hrs and 24hrs.
The following is how my targets file
Order by: Relevance
for complex (ie involving more than 3 samples) loop
designs using two-colour microarrays in the limma documentation.
Although section 20.5 does give an example, with 5 RNA samples, one of
these is a pool which makes an obvious
div class="preformatted">The limma package has a new function topTableF() which ranks genes by
F-statistic.
I am planning to add a feature to topTable() to access
<div class="preformatted">
>To: Pedro L?pez Romero <plopez at="" cnic.es="">
>From: Naomi Altman <naomi at="" stat.psu.edu="">
>Subject: Re: [BioC] implementing limma with several sistematic
effects
>Cc:
>Bcc:
>X-Eudora-Signature: <work>
>Date: Fri, 10 Mar 2006 16:21:54 -0500
>
>I would say that the problem is …
div class="preformatted">Dear list,
I am trying to pull out a contrast for 3-way interaction using limma,
but as I'm pretty new to microarrays I'm puzzling whether I got it
right or not. So far I haven't been able to find much info
I have a dataset with 10 condition vs 20 control samples and am using limma to test for differential expression. Broadly, groups are age/sex matched but have complex medical histories which...I have a dataset with 10 condition vs 20 control samples and am using limma to test for differential expression. Broadly, groups are age/sex matched but have complex medical histories which add...by sampling…
updated 12 months ago • Ali Barry
Hello,
I have a question in relation to limma and how to extract the random intercepts results after running a duplicated correlation.
To summarize, I have DNA methylation...is as follows:
design=model.matrix(~intervention+Age+Batch,data=pheno)
library(limma)
corfit <- duplicateCorrelation(DMFS,design,block=pheno$ID)
fit = lmFit(DMFS, design,max…
updated 5.3 years ago • macsue.jacques
<div class="preformatted">Short story: I ran a PCA on a matrix of counts from an RNA-seq
experiment and then using the voom-tramsformed data, and they're
completely different. I imagine my results will be very different
using DESeq2 vs limma, and I am wondering how to proceed. Here are the
two PCA biplots:
http://imgur.com/a/DBRfE
More background:
I have an RNA-seq experiment with 5 cond…
<div class="preformatted">Dear Scott,
The code below seems to be from Section 8.3 of the User's Guide
(rather
than 8.6).
Yes, the contrast RNA2 for the second model is the same as RNA2-RNA1
in
the first model.
The first model doesn't set the intercept to anything, because it has
no
intercept.
Yes, the batch effect will be adjusted for if you include it in the
model,
and this is true for…
div class="preformatted">
Hi,
I have been looking at backgroundCorrect, method=none in limma and
compared this to files I have manually altered so that the background
values were zero, without using the backgroundCorrect...very different
-
could anyone explain why to me please? Code is below.
Thanks,
Helen
> library(limma)
> files=dir(pattern="*\\.gpr")
> RG=read.maimage…
In the [dream vignette][1] it's described that for an RNA-seq repeated measure design the limma analysis needs two `duplicateCorrelation` rounds, though this differs from the limma user's guide and manual. Below for...M 2
sample_24 ID12 1 sample_24 M 2
and the limma two-round `duplicateCorrelation` analysis code from the vignette, where the…
updated 6.2 years ago • hermidalc
<div class="preformatted">Dear Karl,
This result suggests that you should average your replicate spots (see
the avedups function in
limma) rather than using duplicate correlation. Yes, it almost
certainly results from trying to
do too much with too little data. Either you don't have enough data,
or the model you're fitting
contains too many terms, so that you can't get a reliable estimat…
of m small molecules and n descriptors (e.g. polar surface area, molecular weight), can I use, say, limma to identify descriptors that differ between these two groups? So basically, I would just be using limma on molecular
updated 7.4 years ago • perdedorium
div class="preformatted">Hello everyone.
I am using limma for microarray analysis for some time. Now I am
trying
to use mergeScans function to merge scans made with different
updated 13.9 years ago • Agnieszka Zmienko
Hi,
I am using limma package to perform differential expression of Illumina data. I am wondering if i can get columns of probelist, foldchange...all the three columns mentioned above where the p-values is of my interest. Can i get this by using limma. Thanks
updated 10.6 years ago • Agaz Hussain Wani
Hello,
I am working with RNA Seq samples from an experiment similar to that described in section 9.7 of the limma user guide (multi-level experiments). The difference is that we have multiple fastq files per subject per condition per...I am working with RNA Seq samples from an experiment similar to that described in section 9.7 of the limma user guide (multi-level experiments). The difference …
updated 6.7 years ago • richard.vinisko
Dear Gordon / list,
I would like to compare the correlation between 3 treatments that are compared to the same reference group using the `` genas() `` function present in limma. However, I also used the function `` arrayweights() `` to account for the "consistency" of each array within each treatment group...treatments that are compared to the same reference group using the `` genas() `` functio…
updated 10.3 years ago • Guido Hooiveld
Hi,
I have a question regarding limma-driven microarray analysis.
I have a total of 24 arrays. My experimental design consists in two fixed factors, i.e. "matrix...Hi,
I have a question regarding limma-driven microarray analysis.
I have a total of 24 arrays. My experimental design consists in two fixed factors, i.e. "matrix" (F or G) and "dim" (2 or 3), and what I consider a Random F…
updated 6.7 years ago • David Rengel
you let me know if there are any changes/modifications you would suggest . thanks !
library("limma")
library("edgeR")
\#\#\# reading the expression dataset
eset <- read.delim("mm10.strand.both.count.exons.condense.genes.NOADJ...using the VOOM transformation :
v <- voom(y,design,plot=TRUE)
\#\#\# doing the LINEAR FIT in LIMMA :
fit <- lmFit(v, design)
fit2 &l…
to account for the variation between lineages within categories. I have been using the r package LIMMA to do this as it can support random effects unlike DESeq2. I've gone through the LIMMA User Guide and have been able to get
updated 6.1 years ago • mjgarcia
samples (treatment/no treatment)
within subject for many subjects. Is there a specific method in Limma
for dealing with this situation or is subject just treated as another
factor?
Thanks,
Sean</div
updated 21.4 years ago • Sean Davis
hard time understanding how to pull out the relevant contrasts when using a model with covariates in `` limma ``.
Let's say I have the following gene expression matrix and experimental variables:
<pre>
library(limma)
set.seed(16)
mat...treatment-contrasts" and "group-means" parametrization, but this is what they are called on the limma user guide (section 9.2
updated 7.5 years ago • enricoferrero
As the subject line says, what does the P value of limma with coef=NULL for topTable indicate
updated 2.5 years ago • S
help me. Some time ago I analysed a large time-course two-colour cDNA microarray data set using LIMMA. I followed, to the letter, the instructions in Chapter 9 of the LIMMA user's guide on how to analyse two-coloured data as
updated 11.1 years ago • christy.vanderjagt
I have three independent sample groups. I'm using GSVA to do the enrichment analysis then using limma to fit a model to the GSVA enrichment scores.
library(GSVA)
library(limma)
p <- 10 \#\# number of genes
n <- 45 \#\# number of samples...comparisons, e.g., between group 1vs2, 1vs3, and 2vs3. Is there a way to go about doing this with limma
divide the (MUTA+ConA-MUTN-ConN) by 2?
I got this question when I looked at the following code in Limma user
guide page 46 with the following code for exact same design
> cont.matrix <- makeContrasts(
+ WT.SvsU=WT.S-WT.U...someone could help me out with
what is*>*probably a simple request to someone familar with lm and
Limma.*>**>*I was following*>*8.4 …
<div class="preformatted">Hello,
I'm new to the Bioconductor list, and fairly new to Bioconductor
itself,
so excuse me if the following is a stupid question- I've been looking
around the list and documentation for a while without finding my
answer.
The short version of my question is "What is the most appropriate way
to
determine if microarray-derived gene expression is associated with an…
updated 16.7 years ago • Jon Manning
Hi all:
I am wondering how to perform the regressions `phenotype ~ gene + covariates` in R using `limma` with microarray data.
I know how to regress `gene ~ phenotype + covariates`. For example, if `phenotype` is BMI and `covariates
updated 6.7 years ago • anon20955
Hi,
I'm using Limma for DE of microarray data. But logFC values in the topTable are not correct, and actually I got the minus values of the...Hi,
I'm using Limma for DE of microarray data. But logFC values in the topTable are not correct, and actually I got the minus values of the two
updated 9.1 years ago • Dawn
<div class="preformatted">Dear all,
Is there an easy way to read 300 Imagene files in XML format to Limma?
Your help is highly appreciated.
Sincerely,
Wei Chen, PhD
Assistant Professor
Biostatistics Core, Karmanos Cancer Institute...div class="preformatted">Dear all,
Is there an easy way to read 300 Imagene files in XML format to Limma?
Your help is highly appreciated.
Sincerely,
W…
keywords but I do not seem to find the right thread.
What I want to know is:
- Does limma arrives to a pvalue by using the log2 scale of the normalized array data?
- Does limma arrives to a pvalue using the normalized
<div class="preformatted">Dear Ming,
You are getting a warning because your linear model is
overparametrized.
The AccNum factor already allows every patient to be different, so the
extra variables Race and ER are redundant in a linear model sense.
You
are including effects for every combination of Race and ER, that's
four
levels, so three extra degrees of freedom, so there must be three
co…
piggybacking
>on MArrayLM's existing behavior.
>
>Also, is this the right place for limma questions? It doesn't have
>its own mailing list yet, does it?
>
>Thanks,
>
>Cyrus Harmon
</div
div class="preformatted">Hi
I have a kooperberg bg corrected dataset in limma and I want to coerce
it to an exprSet object so that I can do some other stuff with it. I
have two objects, RG which is a normal
I'm a bit
puzzled why you haven't already tried this, considering that you're
already using limma and are aware of printorder effects.)
Note that GAL file order is not the same as printorder in general, so
you can't just...33:11 +0000
>From: J.delasHeras at ed.ac.uk
>Subject: Re: [BioC] Plate or print-order effects - limma
>To: bioconductor at stat.math.ethz.ch
>
&…
div class="preformatted">Hi,
I am quite insecure if some parts of the analyis I did in Limma are
really
correct and I would highly appreciate if someone could take a look and
give advice. My main concern is that...with a rgn
r2
<0.5 bad, and only 30% of my data remain unflagged.
And this is what I did using Limma:
> targets=readTargets("Targets_basicSat.txt")
> targets
…
K Smyth
Cc: Bioconductor mailing list
Subject: RE: Can I input ordinal variables into a model in Limma?
Thanks very much Gordon.
________________________________________
From: Gordon K Smyth [smyth@wehi.EDU.AU]
Sent...Scott Robinson
Cc: Bioconductor mailing list
Subject: Can I input ordinal variables into a model in Limma?
Dear Scott,
An ordinal variable is just a special case of a categorica…
updated 11.8 years ago • Scott Robinson
div class="preformatted">Dear BioC,
Using limma, when fitting the model:
model.matrix(~Tissue * Pperiod + Time + Animal)
I get this warning:
> fit <- lmFit(rma.pp, design)
Coefficients...factor
for pairing (Animal) trying to fit more factors than my measurements
can
support and this is limma's way of telling me? Raw script and targets
file below.
I really hope an experienced …
and tumor samples but to get the two profiles comparable. I was thinking to use removeBathEffect of limma using Organoids and WT as a batch and correct for this know source of variation. The question is: is it possible to re-use
updated 9.1 years ago • Keifa
possible to test for fold-change in only one direction (LFC > 0) using the _treat _function from limma? Similar to using the altHypothesis argument in the _results_ function from DESeq2?
I tried myself to introduce some
updated 4.8 years ago • s1437643
avoid losing a sample as reference running an
> individual differential expression analysis (LIMMA)
> To: bioconductor at stat.math.ethz.ch
>
> Hello listmemebers,
>
>
> I have data from two-color microarray expression...also like to
run
> an individual analysis making all pair-wise comparisons. I'm using
the
> LIMMA package in …
updated 16.9 years ago • Gordon Smyth
I have RNA-seq data that has three groups - Control (C), Disease1 (D1), and Disease2 (D2). The patients of D1 and D2 were treated with a drug (T) and data was generated on pre- and post-treatment disease groups i.e. I have 5 grouping factors - C, D1-pre, D1-post, D2-pre, D2-post. I am a bit confused while modeling this nested data to identify DE genes in limma. I have two questions in mind:
1. Wh…
updated 3.8 years ago • AST
coefficients and associated error with
the most significant genes that come out as result of LIMMA (lmfit,
contrasts.fit, eBayes). I thought that it should be stdev.unscaled,
but
this seems to be the same for all the genes
updated 15.6 years ago • Daniel Brewer
Hi,
I am doing pairwise RNA-Seq comparisons between 3 groups in limma. Looking at the manual it seems like this is best done with the contrasts. However, I wanted to compare the results using...contrasts with the results doing just group 1 vs group 2 in limma. I've noticed some differences in the differential expression results. I understand the P values might be different
updated 6.6 years ago • Jake
i have controls and cases (dosed with a drug). I have used the following in the design matrix for limma:
design <- model.matrix( ~CLASS) )
This creates a design matrix:
<table border="1" cellpadding="1" cellspacing="1" style="width...samples dosed with the drug. Therefore the control group is my reference group.
From my output from limma for each gene i get a logFC. If i h…
updated 8.7 years ago • danielle.newby
a question about correcting for batch effects prior to differential gene expression analysis with limma. I've read that batch effect correction functions such as ComBat should not be used prior to differential expression...analysis in limma, and that batch effects should be accounted for in linear modeling instead. However, in my case a batch effect and...to raw data using libra…
updated 8.6 years ago • adscheid3
<div class="preformatted">You could do this using LME. It will be slow.
--Naomi
At 05:47 AM 6/2/2005, HAG wrote:
>Dear list,
>
>I have an experiment with 24 arrays.
>I have 3 factors each with 2 levels and 12 blocks
(1,1,2,2,3,3,....,12,12).
>Each gene is replicated 4 times on each array.
>
>I know how to fit blocks as random as explained …
<div class="preformatted">Dear Gordon,
Thanks for the answer. I've been working on these data for some time.
It was obvious how to extract DGE for treatment vs control (just
looking at the coefficient names), nevertheless I still do not get how
to find genes that change between two experimental groups and the
control. I would like to use makeContrasts in order to explicitly
define the possi…
<div class="preformatted">Hi Guido,
> Date: Mon, 31 Mar 2014 19:20:34 +0000
> From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl="">
> To: "bioconductor at r-project.org" <bioconductor at="" r-project.org="">
> Subject: [BioC] queries re Voom + Limma for RNA-seq data
>
> Hello Gordon and all,
> I am analyzing a RNA-seq experim…
updated 11.8 years ago • Gordon Smyth
on my RNA-Seq data leaving the
data as cpm-log2 normalized. How do I use this as input in limma? It
usually only take count data.
-- output of sessionInfo():
none
--
Sent via the guest posting facility at bioconductor.org
updated 11.3 years ago • Guest User
div class="preformatted">I would like to know why some of you bioconductorians are using Limma
and
some are using Sam. I find some quite convinient and the theory seems
straightforward in a statistical sense. Please
updated 21.0 years ago • Auer Michael
div class="preformatted">Dear Limma users,
Your suggestions,comments, thoughts appreciated on this posting.
Here is an experimental design with 2 sites...in single channels in order to
exclude
the technical duplicate controls from either Cy5 or Cy3? The limma
user
guide (page 88) gave an example involving a composite design
(reference and
direct comparison) where all treated
of the newer DNA methylation
array
> technologies, so you should ask someone who has how well the limma
pipeline
> seems to work on that type of data.
>
> For example, Alicia Oshlack's group develops methods for methylation...gt; arrays and finds limma useful:
>
> http://genomebiology.com/content/13/6/R44
>
> It seems very reasonable to me …
updated 12.1 years ago • Gustavo Fernández Bayón
the input data is clearly wrong
does
not constitute a bug in the software.
The latest versions of limma set the 'genes' component directly from
the
gpr files. This means that there is no longer any need to read the
GAL
file with
analysis in general.
I am using Windows XP and R version 2.5.1.
I have a few questions about the limma package that I am using for
cDNA array analysis.
First: I would like to flag out all spots with fluorescence intensity
updated 18.3 years ago • Brooke LaFlamme
<div class="preformatted">Hi,
I just wanted to make a note of a small issue that if you use 'limma'
combined with 'arrayQualityMetrics' there is a masking of some
functions
caused by the loaded package dependency 'beadarray...div class="preformatted">Hi,
I just wanted to make a note of a small issue that if you use 'limma'
combined with 'arrayQualityMetrics' there is a masking of some
fu…
updated 17.0 years ago • Marcus Davy
I want to conduct a differential expression analysis over bulk RNA-seq data, using the limma package. There are several guides for this package, but non of them is helping me get good results, I don't know if I'm doing
updated 3.7 years ago • loainaom
MASS
"2.3.2" "2.3.1" "2.3.1" "0.15-11" "7.2-34"
statmod sma limma Hmisc
"1.3.0" "0.5.15" "2.10.0" "3.4-1"
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity
updated 18.5 years ago • Al Ivens
class="preformatted">Hi,
Maybe a naive question, but is it possible to do a 'one sample t-test'
in limma while including a covariate in the model? If so, how?
I have an experiment in which 32 volunteers were profiled on array
<div class="preformatted">Dear limma users,
I am trying to analyze a 2x2 factorial experiment with Agilent two-
color
arrays (with direct design). I noticed (from...div class="preformatted">Dear limma users,
I am trying to analyze a 2x2 factorial experiment with Agilent two-
color
arrays (with direct design). I noticed
Recent ...
Replies
Answer: Guitar R package requires update due to dependency GenomicFeatures
by
Kevin Blighe
★
4.0k
Greetings,
This issue is indeed caused by recent changes in the Bioconductor 3.20+ release cycle. The function makeTxDbFromGFF() was previ…
Answer: ATACseq rudimentary questions
by
Kevin Blighe
★
4.0k
For differential analysis tools like DiffTF and TOBIAS, the standard and statistically sound approach is to create **one large consensus pe…
Answer: Clarification on counting in Rsubread (featureCounts)
by
Kevin Blighe
★
4.0k
Dear Luca,
This is a very plausible behavior caused by **read assignment ambiguity** due to **overlapping gene coordinates** (specifical…
Answer: How to install packages such as TCGAbiolinks, SumarizedExperiment?
by
Gordon Smyth
53k
The warning message is telling you that you already have the packages installed.
However, you might consider upgrading to the current vers…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
Frank
•
0
Created by French developer Julien "Orteil" Thiennot, Cookie Clicker transformed the gaming landscape by introducing a new genre of idle ga…
Votes
Awards
• All
Teacher to
Gordon Smyth
53k
Popular Question to
shepherl
4.2k
Popular Question to
Hervé Pagès
16k
Popular Question to
Istvan Albert
▴
50
Locations
• All
United States, 6 minutes ago
United States, 21 minutes ago
The Netherlands, 47 minutes ago
United States, 48 minutes ago
United States, 1 hour ago
United States, 6 minutes ago
United States, 21 minutes ago
The Netherlands, 47 minutes ago
United States, 48 minutes ago
United States, 1 hour ago
Traffic: 2826 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6